The purpose of this research study is to determine the safety of a new method of disease treatment called gene therapy. In this study a modified virus called adeno-associated virus (AAV vector) will be used to transfer a normal gene for human clotting factor IX into patients with severe hemophilia B. Pre-clinical studies in mice and hemophilic dogs have shown that introduction of an AAV vector expressing blood coagulation Factor IX into skeletal muscle can result in sustained expression of Factor IX (F.IX) at levels high enough to ameliorate the hemophilic phenotype (PNAS 94:5804-09, 1997; Nature Med 5: 56-63, 1999). Based on these data and additional pre-clinical studies demonstrating an absence of vector-related toxicity, a clinical study of intramuscular injection of an AAV vector expressing human F.IX (AAV-hFIX) has been initiated in adults with severe hemophilia B. The trial is an open-label, dose escalation study, with 3 patients in each of 3 dose cohorts. The primary purpose of the study is to assess the safety of AAV-hFIX administered intramuscularly. Toxicity related to the delivery of AAV-hFIX will be evaluated locally and systemically. A secondary objective of this study is to evaluate the potential efficacy of AAV-hFIX in each dose group by measuring the biologic activity of the transgene product.